The girl's coach said an official had called her over-the-knee dress "too seductive".
A Facebook post detailing the incident was shared widely, causing outrage.
The Malaysian Chess Federation told local media the accusation was under investigation.
The girl was participating in last month's National Scholastic Chess Championship in Putrajaya, just south of Kuala Lumpur.
Afterwards, her coach, Kaushal Khandhar, wrote a long public Facebook post saying an arbiter interrupted her game to tell her she was violating the competition's dress code.